Early colonization by Enterobacteriaceae in the developing gut microbiota of preterm infants: A culture-based insight

The gut microbiome plays a significant role in human health and disease pathogenesis. In preterm infants, gut dysbiosis often results in early dominance of opportunistic pathogens, particularly members of the Enterobacteriaceae family. Enterobacteriaceae can serve as potential reservoirs of opportunistic pathogens, antibiotic-resistance determinants and may contribute to major neonatal morbidities, including necrotizing enterocolitis (NEC) and late-onset sepsis (LOS). This study aims to isolate and identify Enterobacteriaceae, as well as to explore the diversity of isolated Klebsiella pneumoniae from meconium/early stool samples of preterm infants collected from a neonatal intensive care unit (NICU) in Johor Bahru, Malaysia. A combination of culture-based isolation technique, phenotypic and genotypic identification methods was used to identify the culturable Enterobacteriaceae in the gut of preterm infants. Three main bacterial families were successfully isolated and identified from the stool samples of preterm infants, which include Enterobacteriaceae, 46% (76/166 isolates), Staphylococcaceae, 22% (37/166), Enterococcaceae, 22% (37/166) and others, 10% (16/166). It was clear that Enterobacteriaceae was one of the predominant bacterial groups during the early gut colonization in preterm infants, making up to 46% of all isolates. Within the Enterobacteriaceae family, K. pneumoniae, 74% (56/76 isolates) dominates, followed by Escherichia coli, 15% (11/76), Klebsiella aerogenes, 9% (7/76), Citrobacter europaeus, 1% (1/76), and Citrobacter freundii, 1% (1/76). The high number of Enterobacteriaceae isolates, particularly K. pneumoniae, followed by E. coli are concerning as these bacterial species are often associated with hospital-acquired infections in the NICU. Our findings provide insight into the early gut colonization patterns of culturable gut bacteria in preterm infants. It highlights the importance of continuous microbiological monitoring and infection control measures within the NICU to mitigate potential Enterobacteriaceae-associated infections.